Pyphe, a python toolbox for assessing microbial growth and cell viability in high-throughput colony screens

Microbial fitness screens are a key technique in functional genomics. We present an allin-one solution, pyphe, for automating and improving data analysis pipelines associated with largescale fitness screens, including image acquisition and quantification, data normalisation, and statistical analysis. Pyphe is versatile and processes fitness data from colony sizes, viability scores from phloxine B staining or colony growth curves, all obtained with inexpensive transilluminating flatbed scanners. We apply pyphe to show that the fitness information contained in late endpoint measurements of colony sizes is similar to maximum growth slopes from time series. We phenotype gene-deletion strains of fission yeast in 59,350 individual fitness assays in 70 conditions, revealing that colony size and viability provide complementary, independent information. Viability scores obtained from quantifying the redness of phloxine-stained colonies accurately reflect the fraction of live cells within colonies. Pyphe is user-friendly, open-source and fully documented, illustrated by applications to diverse fitness analysis scenarios

High precision measurement of the hyperfine fields of substitutional and defect associated Cd in single crystalline hcp cobalt

The hyperfine fields of Cd in single crystalline hcp Co were measured after simultaneous implantation of 111mCd and 111In. High statistics measurements could be done separately for each parent isotope combining the e--g and g-g PAC techniques. The hyperfine coupling constants wL(CdCo)=422.8(1) Mrad/s and w0(CdCo)=6.14(11) Mrad/s are determined for Cd probes in undisturbed substitutional sites. Several defect associated sites in the hcp Co lattice are clearly seen in the data. Most of the radiation damage created by the ion implantation anneals out at temperatures below 503 K, with only one dominating component surviving at this temperature. This defect is assigned as a probe atom in an interstitial site, surrounded by a vacancy tetrahedron. The corresponding magnetic field and electric field gradient are collinear with the c-axis of the Co lattice, and the respective coupling constants are wL(defect)= 216.7(2) Mrad/s and w0(defect)= 45.3(6) Mrad/s

On-line perturbed angular correlation studies with the short lived 127Cs^{127} Cs probe

On-line Perturbed Angular Correlation (PAC) experiments were performed on the 66.0 keV excited state of 127 Cs, using the gamma(114.7 keV)-eL (66.0 keV) cascade from the decay of the short-lived 127 Ba (T1/2=13 min) isotope produced at the ISOLDE facility at CERN. The PAC experiments were performed with an optimized g-e spectrometer coupled to the ISOLDE beam line, which allowed simultaneous implantation and measurement. The optimization of the experiment is described and the first results on metallic foils and single crystals of Al, Be, Ga, Zn, and Ni are presented and discussed. The derived nuclear moments of the 66.0 keV excited state of 127 Cs are |miu| = 2.9(2) miuN and |Q| = 0.58(12)b. Applications of this new PAC isotope are outlined

Staghorn Calculi: an Unusual and Serious Clinical Case

Introdução: Este artigo tem como objectivo apresentar um caso clínico de litíase coraliforme que exemplifica a gravidade resultante desta patologia. Caso Clínico: Caso clínico de uma doente do sexo feminino, 43 anos, sem antecedentes pessoais de relevo, que recorreu ao Serviço de Urgência por prostração, astenia e anorexia. Foi-lhe diagnosticada insuficiência renal grave, litíase coraliforme bilateral e hidronefrose com conteúdo não puro no excretor. A doente foi submetida a colocação bilateral de nefrostomias e uma semana depois, num contexto de pionefrose à esquerda e sépsis, foi submetida a nefrectomia total à esquerda. Ficou a realizar hemodiálise em ambulatório. Posteriormente concluiu-se perda irreversível da função renal, com consequente nefrectomia direita. Discussão: Este caso constitui um exemplo da gravidade resultante da litíase coraliforme. Mesmo sem manifestação clínica prévia, pode causar insuficiência renal avançada, com infecção urinária grave e sépsis que colocam a vida em risco

Ocorrência de espécies daninhas no cultivo de soja em função da tecnologia de manejo.

JIPE 2013

Avaliação da micropropagação de dois genótipos de palma forrageira.

O objetivo deste trabalho foi avaliar a multiplicação in vitro de dois genótipos de palma forrageira [Opunt ia tuna (L.) Mill var. Orelha de Elefante e Nopalea cochenillifera Salm Dyck var. Mão de Moça], no período de julho de 2014 a março de 2015

Reação à antracnose do feijoeiro-comum em ensaio de campo com inoculação artificial.

O programa de melhoramento do feijoeiro conduzido pela Embrapa e parceiros tem sido bem sucedido no desenvolvimento de linhagens resistentes à antracnose. As cultivares BRS Cometa e BRS Horizonte, as quais possuem grãos do tipo carioca, os de maior aceitação pelo mercado consumidor brasileiro, são exemplos deste sucesso.CONAF

Shedding light on the african enigma: In vitro testing of homo sapiens-helicobacter pylori coevolution

The continuous characterization of genome-wide diversity in population and case- cohort samples, allied to the development of new algorithms, are shedding light on host ancestry impact and selection events on various infectious diseases. Especially interesting are the longstanding associations between humans and certain bacteria, such as the case of Helicobacter pylori, which could have been strong drivers of adaptation leading to coevolution. Some evidence on admixed gastric cancer cohorts have been suggested as supporting Homo-Helicobacter coevolution, but reliable experimental data that control both the bacterium and the host ancestries are lacking. Here, we conducted the first in vitro coinfection assays with dual humanand bacterium-matched and -mismatched ancestries, in African and European backgrounds, to evaluate the genome wide gene expression host response to H. pylori. Our results showed that: (1) the host response to H. pylori infection was greatly shaped by the human ancestry, with variability on innate immune system and metabolism; (2) African human ancestry showed signs of coevolution with H. pylori while European ancestry appeared to be maladapted; and (3) mismatched ancestry did not seem to be an important differentiator of gene expression at the initial stages of infection as assayed here.Funds were guaranteed by the project “Advancing cancer research: from basic knowledge to application”; NORTE-01-0145-FEDER-000029; Projetos Estruturados de I & D & I, funded by Norte 2020-Programa Operacional Regional do Norte. i3S is financed by FEDER-Fundo Europeu de Desenvolvimento Regional funds through the COMPETE 2020-Competitiveness and Internationalization Operational Programme (POCI), Portugal 2020, and by Portuguese funds through FCT/Ministério da Ciência, Tecnologia e Inovação in the framework of the project “Institute for Research and Innovation in Health Sciences” (POCI-01-0145-FEDER-007274)